diff --git a/src/main/java/fr/pasteur/ida/zellige/Main.java b/src/main/java/fr/pasteur/ida/zellige/Main.java
index 787eac3bb89bbc3944f452f20b551a8af76ff571..d4370e98ce1502bd46d78854661bd4043b1568c4 100644
--- a/src/main/java/fr/pasteur/ida/zellige/Main.java
+++ b/src/main/java/fr/pasteur/ida/zellige/Main.java
@@ -80,364 +80,13 @@ import static fr.pasteur.ida.zellige.utils.Util.create4dimImage;
public class Main
{
- private final static Logger LOGGER = LoggerFactory.getLogger( Main.class );
- private static final String SEMI_COLON_DELIMITER = ";";
- private static final int RADIUS = 2;
- private static final String FILTER = "GaussianBlur";
- private static final int CONNEXITY = 4;
- private static LogFile fileAppender;
- @SuppressWarnings( "unchecked" )
- public static < T extends RealType< T > & NativeType< T > > void main( String[] args ) throws Exception
-
- {
-// // Launch ImageJ.
-//
-//
-// // Input of the image.
-// final String imagePath = "doc/Scan1_volume_crop.tif";
-// //args[ 0 ]; /* The image path goes here !!!! */
-// //args[ 0 ]; /* The image path goes here !!!! */
-// LOGGER.debug( imagePath );
-// /* JY version for opening files. */
-//// final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );
-//// final Img< T > stackImage = ( Img< T > )
-// IO.openAll( imagePath ).get( 0 ).getImg();
-//// Load the image.
-//
-// // Launch ImageJ.
-// ImageJ ij = new ImageJ();
-// ij.launch( args );
-// String currentFolder = FileSystems.getDefault()
-// .getPath( "" )
-// .toAbsolutePath()
-// .toString();
-// String imageFilePath = "doc/Cochlée1.tif";
-// Object obj = ij.io().
-// open( new File( currentFolder, imageFilePath ).getAbsolutePath() );
-//
-// // Display it.
-// ij.ui().show( obj );
-// Dataset dataset = ij.imageDisplay().getActiveDataset( ij.context().getService( ImageDisplayService.class ).getImageDisplays().get( 0 ) );
-//
-// final Img< T > stackImage = ( Img< T > ) dataset.getImgPlus().getImg();
-//
-// //final Img< T > stackImage = ( Img< T > ) imgPlus.getImg();
-//// final Img< ? > image = imgPlus.getImg();
-// int i = -1;
-// /* User Parameters AKA arguments to run the program*/
-//// int bin = Integer.parseInt( args [i++=)] );//TODO order of arguments
-//// int channel = Integer.parseInt(args [i++] );
-//// int amplitude = Integer.parseInt( args [i++] );
-//// int otsu = Integer.parseInt( args [i++] );
-//// int islandSize = Integer.parseInt( args [i++] );
-//// int connexity = Integer.parseInt( args [i++] );
-//// double sigmaXY = Double.parseDouble( args [i++] );
-//// double sigmaZ = Double.parseDouble( args [i++] );
-//// double startingOsSize1 = Double.parseDouble( args [i++] );
-//// int overlap1 = Integer.parseInt( args [i++] );
-//// double connexityRate1 = Double.parseDouble( args [i++] );
-//// double startingOsSize2 = Double.parseDouble( args [i++] );
-//// int overlap2 = Integer.parseInt( args [i++] );
-//// double connexityRate2 = Double.parseDouble( args [i++] );
-//// double surfaceMinSizeFactor = Double.parseDouble( args [i++] );
-//// int delta = Integer.parseInt( args [i++] );
-// /* End of parameters. */
-//
-//
-// int bin = 2;//TODO order of arguments
-// int channel = 0;
-// int amplitude = 10;
-// int otsu = 10;
-// int islandSize = 5;
-// int connexity = 4;
-// double sigmaXY = 3;
-// double sigmaZ = 1;
-// double startingOsSize1 = 0.7;
-// int overlap1 = 10;
-// double connexityRate1 = 0.6;
-// double startingOsSize2 = 0.1;
-// int overlap2 = 5;
-// double connexityRate2 = 0.9;
-// double surfaceMinSizeFactor = 0.4;
-// int delta = 2;
-// // Fixed parameters for now...
-// String filter = "GaussianBlur";
-// double filterParameter = 2;
-//
-//
-// /* Print parameters.*/
-// LOGGER.info( "Input image : " + imagePath );
-// LOGGER.info( "Preprocessing Parameters" );
-// LOGGER.info( "------------------------" );
-// LOGGER.info( "bin = {}", bin );
-// LOGGER.info( "Channel: {}", channel );
-// LOGGER.info( "filter : {}", filter );
-// LOGGER.info( "filter parameter : {}", filterParameter );
-// LOGGER.info( "Selection Parameters" );
-// LOGGER.info( "------------------------" );
-// LOGGER.info( "amplitude : {}", amplitude );
-// LOGGER.info( "threshold : {}", otsu );
-// LOGGER.info( "connexity : {}", connexity );
-// LOGGER.info( "island size : {}", islandSize );
-// LOGGER.info( "sigmaXY : {}", sigmaXY );
-// LOGGER.info( "sigmaZ : {}", sigmaZ );
-// LOGGER.info( "Construction Parameters" );
-// LOGGER.info( "------------------------" );
-// LOGGER.info( "starting os size1 : {}", startingOsSize1 );
-// LOGGER.info( "overlap1 :{}", overlap1 );
-// LOGGER.info( "connexityRate1 :{}", connexityRate1 );
-// LOGGER.info( "starting os size2 : {}", startingOsSize2 );
-// LOGGER.info( "overlap2 :{}", overlap2 );
-// LOGGER.info( "connexityRate2 :{}", connexityRate2 );
-// LOGGER.info( "surface Minimum size factor : {}", surfaceMinSizeFactor );
-// LOGGER.info( "Projection Parameters" );
-// LOGGER.info( "------------------------" );
-// LOGGER.info( "delta : {}", delta );
-// LOGGER.info( System.lineSeparator() );
-// /* End of Print parameters.*/
-//
-// PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( filter, filterParameter, bin );
-// ClassificationParameters classificationParameters = new ClassificationParameters( amplitude, otsu );
-// PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, islandSize, connexity );
-// ProjectionParameters projectionParameters = new ProjectionParameters( delta, "MIP" );// no other method implemented yet.
-// ConstructionParameters[] constructionParameters = new ConstructionParameters[]{
-// new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor ),
-// new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor ) };
-//
-//
-// DisplayParameters displayParameters = new DisplayParameters(
-// true,
-// false,
-// false,
-// true,
-// false, false );
-// IJ.log( "Type: " + stackImage.firstElement().getClass().toGenericString() );
-//
-// if ( stackImage.numDimensions() == 3 )// Is it a stack ?
-// {
-// Img< T > temp = Util.create4dimImage( dataset );
-// RandomAccessibleInterval< T > input = Views.hyperSlice( temp, 2, channel );
-// ReferenceSurfaceExtraction< T > rse = new ReferenceSurfaceExtraction<>
-// ();
-// rse.select( input, pretreatmentParameters, classificationParameters, postTreatmentParameters );
-// rse.construct( input, ( ( Img< T > ) dataset.getImgPlus().getImg() ).factory(), constructionParameters );
-// if ( ! GraphicsEnvironment.isHeadless() )
-// {
-// try
-// {
-// rse.project( projectionParameters, displayParameters );
-// }
-// catch ( Exception e )
-// {
-// LOGGER.debug( e.getMessage() );
-// }
-// }
-// }
-// else
-// {
-// LOGGER.debug( " This image has to be a z-stack ! " );
-// }
-
- // Launch ImageJ.
- ImageJ ij = new ImageJ();
-// ij.launch( args );
- String CSV_FILE = "doc/test.csv"; //args[ 0 ];
- setLogStatus();
- try ( Stream< String > lines = Files.lines( Paths.get( CSV_FILE ) ) )
- {
- List< List< String > > records = lines.map( line -> Arrays.asList( line.split( SEMI_COLON_DELIMITER ) ) )
- .collect( Collectors.toList() );
- LOGGER.debug( "the csv is loaded" );
- for ( int i = 1; i < records.size(); i++ ) // skip the header
- {
- List< String > line = records.get( i );
- // Input
- String inputPath = line.get( 0 );
- Dataset dataset = ArgumentCheck.input( ij.scifio().datasetIO().open( inputPath ) );
- String inputName = FilenameUtils.removeExtension(dataset.getName());
- String id = uniqueID();
- Path datasetLocation = Paths.get(inputPath).getParent();
-
- Path outputPath = Files.createDirectories(Paths.get(String.format("%s\\%s%s",datasetLocation.toString() , inputName, id)));
- setLogFilePath( String.format("%s\\log.txt", outputPath) );
-
- int nbChannel = ( int ) dataset.getChannels() > 0 ? ( int ) dataset.getChannels(): 1;
- ArrayList<ColorTable> colorTables = new ArrayList<>();
- for ( int channel = 0; channel < nbChannel ; channel++ )
- {
- colorTables.add(dataset.getImgPlus().getColorTable( channel ));
- }
-
- // Preprocessing Parameters
- LOGGER.info( "Preprocessing parameters" );
- LOGGER.info( "------------------------" );
- int bin = ArgumentCheck.bin( line.get( 1 ) );
- int channel = ArgumentCheck.channel( line.get( 2 ), nbChannel );
-
-
- // Selection Parameters
- LOGGER.info( "Selection parameters" );
- LOGGER.info( "--------------------" );
- int amplitude = ArgumentCheck.amplitude( line.get( 3 ) );
- int otsu = ArgumentCheck.otsu( line.get( 4 ) );
- int islandSize = ArgumentCheck.islandSize( line.get( 5 ) );
- double sigmaXY = ArgumentCheck.sigmaXY( line.get( 6 ) );
- double sigmaZ = ArgumentCheck.sigmaZ( line.get( 7 ) );
-
- // Construction Parameters
- LOGGER.info( "Construction parameters" );
- LOGGER.info( "-----------------------" );
- int FIRST_ROUND = 1;
- double startingOsSize1 = ArgumentCheck.startingOsSize( line.get( 8 ), FIRST_ROUND );
- int overlap1 = ArgumentCheck.overlap( line.get( 9 ), FIRST_ROUND );
- double connexityRate1 = ArgumentCheck.connexity( line.get( 10 ), FIRST_ROUND );
- int SECOND_ROUND = 2;
- double startingOsSize2 = ArgumentCheck.startingOsSize( line.get( 11 ), SECOND_ROUND );
- int overlap2 = ArgumentCheck.overlap( line.get( 12 ), SECOND_ROUND );
- double connexityRate2 = ArgumentCheck.connexity( line.get( 13 ), SECOND_ROUND );
- double surfaceMinSizeFactor = Double.parseDouble( line.get( 14 ) );
-
- // Projection Parameters
- LOGGER.info( "\nProjection parameters" );
- LOGGER.info( "--------------------" );
- ArrayList< ProjectionParameters > projectionParameters = new ArrayList<>();
- for ( int n = 0; n < nbChannel; n++ )
- {
- LOGGER.info( " Channel {}", (n+1 ));
-// int channelNb = n * 1;
- int delta = ArgumentCheck.delta( line.get( 15 + (3 * n) ), n );
- int offset = ArgumentCheck.offset( line.get( 16 + (3 * n) ), n );
- String method = ArgumentCheck.method( line.get( 17 +(3 * n) ), n );
- ProjectionParameters parameters = new ProjectionParameters( delta, offset, method );
- projectionParameters.add( parameters );
- }
- LOGGER.debug( "All argument are checked." );
-
- //Parameters
- PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( FILTER, RADIUS, bin );
- ClassificationParameters classificationParameters = new ClassificationParameters( amplitude, otsu );
- PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, islandSize, CONNEXITY );
- ConstructionParameters[] constructionParameters = new ConstructionParameters[2];
- constructionParameters [0] = new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor );
- constructionParameters [1] = new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor );
-
- //set the input
- Img<T> input ;
- if ( nbChannel == 1 )
- {
- try
- {
- input = ( create4dimImage( dataset ) );
- }
- catch ( Exception e )
- {
- throw new RuntimeException( e );
- }
- }
- else
- {
- input = ( ( Img< T > ) dataset.getImgPlus() );
- }
-
- // Set the target channel
- RandomAccessibleInterval<T> inputChannel = Views.hyperSlice( input, 2, (channel -1) );
-
- // Preprocessing and selection steps
- ImageJFunctions.show(input, "input");
- Img <FloatType > selectedPixels = Selection.run(inputChannel, pretreatmentParameters, classificationParameters, postTreatmentParameters);
-
- // Construction step
- ArrayList< ReferenceSurface< T > > referenceSurfaces = Construction.run(constructionParameters, input, input.factory(), selectedPixels, bin);
-
- // Projection step
- ArrayList<ImgPlus<T>> finalProjections = new ArrayList<>();
-
- for ( int j = 0; j < referenceSurfaces.size(); j++ )
- {
- ArrayList<Img<T>> channelProjections = new ArrayList<>();
- Img< UnsignedShortType > zMap = referenceSurfaces.get(j).getzMap();
- for ( int k = 0; k < nbChannel; k++ )
- {
- ProjectionParameters projectionParameter = projectionParameters.get( 0 );
- RandomAccessibleInterval<T> channelImg = Views.hyperSlice( input, 2, k );
- Img<T> subVolume = ReferenceSurfaceProjection.getSubStack( channelImg, input.factory(),zMap, projectionParameter.getDelta(), projectionParameter.getOffset());
-
- Img<T> p = ReferenceSurfaceProjection.run( subVolume, projectionParameter.getProjectionMethod() );
- channelProjections.add(k, p );
- }
- Img<T> temp = ReferenceSurfaceProjection.regroupChannels( channelProjections );
- String projectionName = String.format( "%s_proj_%d", inputName, (j+1) );
- ImgPlus< T > finalProjection = ReferenceSurfaceProjection.setColorsAndName( temp, colorTables, projectionName );
- finalProjections.add( finalProjection );
- }
- ImgSaver saver = new ImgSaver();
- for ( int j = 0; j < referenceSurfaces.size(); j++ )
- {
- ImgPlus<T> projection = finalProjections.get(j);
- String imgLocation = String.format( "%s\\%s%s",outputPath , projection.getName(), ".tif");
- saver.saveImg(imgLocation, projection ) ;
- }
- LOGGER.debug("End of process");
- fileAppender.stop();
- }
- }
- }
-
- /**
- * Creates a new LogAppender to display the program state in the GUI.
- */
- public static void setLogStatus()
- {
- LoggerContext context = ( LoggerContext ) LoggerFactory.getILoggerFactory();
- ch.qos.logback.classic.Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME);
-
- // Encoder
- PatternLayoutEncoder encoder = new PatternLayoutEncoder();
- encoder.setContext( context );
- encoder.setPattern( "%msg%n" );
- encoder.start();
-
- // Creates a new FileAppender
- fileAppender = new LogFile();
- fileAppender.setContext( context );
- fileAppender.setFile( ".\\log.txt" );
-
- fileAppender.setEncoder( encoder );
- fileAppender.start();
-
- // Attach the appender to the logger
- rootLogger.addAppender( fileAppender );
-
- }
-
- public static void setLogFilePath(String path)
- {
- fileAppender.stop();
- fileAppender.setFile( path );
- fileAppender.start();
- }
+ @SuppressWarnings( "unchecked" )
- public static String uniqueID()
+ public static < T extends RealType< T > & NativeType< T > > void main( String [] args ) throws Exception
{
- RandomStringGenerator generator = new RandomStringGenerator.Builder()
- .withinRange('A', 'Z').get();
- RandomStringGenerator generator2 = new RandomStringGenerator.Builder()
- .withinRange('1', '9').get();
- return String.format("_%s%s", generator.generate(2), generator2.generate(2));
+ String CSV_FILE ="doc/test.csv";
+ ReferenceSurfaceExtraction.run( CSV_FILE );
}
- public static class LogFile extends FileAppender< ILoggingEvent >
- {
- @Override
- protected void append( ILoggingEvent iLoggingEvent )
- {
- String level = iLoggingEvent.getLevel().toString();
- if ( level.equals( Level.INFO.toString() ) )
- {
- super.append(iLoggingEvent);
- }
-
- }
- }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java b/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
index 7150890f25dff0d0cb4676dbc04bb6abecb2d152..b0d63bcb125c76ce735e5f0d5f6e8458bde82cb7 100644
--- a/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
@@ -28,8 +28,16 @@
*/
package fr.pasteur.ida.zellige;
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.LoggerContext;
+import ch.qos.logback.classic.encoder.PatternLayoutEncoder;
+import ch.qos.logback.classic.spi.ILoggingEvent;
+import ch.qos.logback.core.FileAppender;
import fr.pasteur.ida.zellige.element.ReferenceSurface;
import fr.pasteur.ida.zellige.element.Surface;
+import fr.pasteur.ida.zellige.gui.exception.NoA3DStackException;
+import fr.pasteur.ida.zellige.gui.exception.TimeLapseException;
+import fr.pasteur.ida.zellige.steps.construction.Construction;
import fr.pasteur.ida.zellige.steps.construction.ConstructionCompletion;
import fr.pasteur.ida.zellige.steps.construction.exception.NoSurfaceFoundException;
import fr.pasteur.ida.zellige.steps.construction.rounds.ConstructionParameters;
@@ -44,27 +52,53 @@ import fr.pasteur.ida.zellige.steps.selection.classification.ClassificationParam
import fr.pasteur.ida.zellige.steps.selection.exception.DataValidationException;
import fr.pasteur.ida.zellige.steps.selection.exception.ImageTooLargeException;
import fr.pasteur.ida.zellige.steps.selection.exception.NoClassificationException;
+import fr.pasteur.ida.zellige.steps.selection.exception.ParameterException;
import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatmentParameters;
import fr.pasteur.ida.zellige.steps.selection.pretreatment.PretreatmentParameters;
+import fr.pasteur.ida.zellige.steps.selection.util.ArgumentCheck;
+import io.scif.img.ImgSaver;
+import net.imagej.Dataset;
+import net.imagej.ImageJ;
+import net.imagej.ImgPlus;
import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.display.ColorTable;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
+import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.FloatType;
+import net.imglib2.view.Views;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.text.RandomStringGenerator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
import static fr.pasteur.ida.zellige.steps.selection.util.Derivative.FORWARD;
+import static fr.pasteur.ida.zellige.utils.Util.create4dimImage;
public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( ReferenceSurfaceExtraction.class );
-
+ private static final String SEMI_COLON_DELIMITER = ";";
+ private static final int RADIUS = 2;
+ private static final String FILTER = "GaussianBlur";
+ private static final int CONNEXITY = 4;
+ private static LogFile fileAppender;
+ @SuppressWarnings( "unchecked" )
private final ArrayList< ReferenceSurface< T > > referenceSurfaces = new ArrayList<>();
private Img< FloatType > maximums;
@@ -86,9 +120,234 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
private static final String derivativeMethod = FORWARD;
- public ReferenceSurfaceExtraction( )
+
+
+
+ public static < T extends RealType< T > & NativeType< T > > void run(String CSV_FILE)throws IOException, ParameterException
+ {
+ ImageJ ij = new ImageJ();
+// ij.launch( args );
+ setLogStatus();
+ try ( Stream< String > lines = Files.lines( Paths.get( CSV_FILE ) ) )
+ {
+ List< List< String > > records = lines.map( line -> Arrays.asList( line.split( SEMI_COLON_DELIMITER ) ) )
+ .collect( Collectors.toList() );
+ LOGGER.debug( "the csv is loaded" );
+ for ( int i = 1; i < records.size(); i++ ) // skip the header
+ {
+ List< String > line = records.get( i );
+ // Input
+ String inputPath = line.get( 0 );
+ Dataset dataset = ArgumentCheck.input( ij.scifio().datasetIO().open( inputPath ) );
+ String inputName = FilenameUtils.removeExtension(dataset.getName());
+ String id = uniqueID();
+ Path datasetLocation = Paths.get(inputPath).getParent();
+
+ Path outputPath = Files.createDirectories(Paths.get(String.format("%s\\%s%s",datasetLocation.toString() , inputName, id)));
+ setLogFilePath( String.format("%s\\log.txt", outputPath) );
+
+ int nbChannel = ( int ) dataset.getChannels() > 0 ? ( int ) dataset.getChannels(): 1;
+ ArrayList< ColorTable > colorTables = new ArrayList<>();
+ for ( int channel = 0; channel < nbChannel ; channel++ )
+ {
+ colorTables.add(dataset.getImgPlus().getColorTable( channel ));
+ }
+
+ // Preprocessing Parameters
+ LOGGER.info( "Preprocessing parameters" );
+ LOGGER.info( "------------------------" );
+ int bin = ArgumentCheck.bin( line.get( 1 ) );
+ int channel = ArgumentCheck.channel( line.get( 2 ), nbChannel );
+
+
+ // Selection Parameters
+ LOGGER.info( "Selection parameters" );
+ LOGGER.info( "--------------------" );
+ int amplitude = ArgumentCheck.amplitude( line.get( 3 ) );
+ int otsu = ArgumentCheck.otsu( line.get( 4 ) );
+ int islandSize = ArgumentCheck.islandSize( line.get( 5 ) );
+ double sigmaXY = ArgumentCheck.sigmaXY( line.get( 6 ) );
+ double sigmaZ = ArgumentCheck.sigmaZ( line.get( 7 ) );
+
+ // Construction Parameters
+ LOGGER.info( "Construction parameters" );
+ LOGGER.info( "-----------------------" );
+ int FIRST_ROUND = 1;
+ double startingOsSize1 = ArgumentCheck.startingOsSize( line.get( 8 ), FIRST_ROUND );
+ int overlap1 = ArgumentCheck.overlap( line.get( 9 ), FIRST_ROUND );
+ double connexityRate1 = ArgumentCheck.connexity( line.get( 10 ), FIRST_ROUND );
+ int SECOND_ROUND = 2;
+ double startingOsSize2 = ArgumentCheck.startingOsSize( line.get( 11 ), SECOND_ROUND );
+ int overlap2 = ArgumentCheck.overlap( line.get( 12 ), SECOND_ROUND );
+ double connexityRate2 = ArgumentCheck.connexity( line.get( 13 ), SECOND_ROUND );
+ double surfaceMinSizeFactor = Double.parseDouble( line.get( 14 ) );
+
+ // Projection Parameters
+ LOGGER.info( "\nProjection parameters" );
+ LOGGER.info( "--------------------" );
+ ArrayList< ProjectionParameters > projectionParameters = new ArrayList<>();
+ for ( int n = 0; n < nbChannel; n++ )
+ {
+ LOGGER.info( " Channel {}", (n+1 ));
+// int channelNb = n * 1;
+ int delta = ArgumentCheck.delta( line.get( 15 + (3 * n) ), n );
+ int offset = ArgumentCheck.offset( line.get( 16 + (3 * n) ), n );
+ String method = ArgumentCheck.method( line.get( 17 +(3 * n) ), n );
+ ProjectionParameters parameters = new ProjectionParameters( delta, offset, method );
+ projectionParameters.add( parameters );
+ }
+ LOGGER.debug( "All argument are checked." );
+
+ //Parameters
+ PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( FILTER, RADIUS, bin );
+ ClassificationParameters classificationParameters = new ClassificationParameters( amplitude, otsu );
+ PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, islandSize, CONNEXITY );
+ ConstructionParameters[] constructionParameters = new ConstructionParameters[2];
+ constructionParameters [0] = new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor );
+ constructionParameters [1] = new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor );
+
+ //set the input
+ Img<T> input ;
+ if ( nbChannel == 1 )
+ {
+ try
+ {
+ input = ( create4dimImage( dataset ) );
+ }
+ catch ( Exception e )
+ {
+ throw new RuntimeException( e );
+ }
+ }
+ else
+ {
+ input = ( ( Img< T > ) dataset.getImgPlus() );
+ }
+
+ // Set the target channel
+ RandomAccessibleInterval<T> inputChannel = Views.hyperSlice( input, 2, (channel -1) );
+
+ // Preprocessing and selection steps
+ ImageJFunctions.show(input, "input");
+ Img <FloatType > selectedPixels = Selection.run(inputChannel, pretreatmentParameters, classificationParameters, postTreatmentParameters);
+
+ // Construction step
+ ArrayList< ReferenceSurface< T > > referenceSurfaces = Construction.run(constructionParameters, input, input.factory(), selectedPixels, bin);
+
+ // Projection step
+ ArrayList< ImgPlus<T> > finalProjections = new ArrayList<>();
+
+
+ for ( int j = 0; j < referenceSurfaces.size(); j++ )
+ {
+ ArrayList<Img<T>> channelProjections = new ArrayList<>();
+ Img< UnsignedShortType > zMap = referenceSurfaces.get(j).getzMap();
+ for ( int k = 0; k < nbChannel; k++ )
+ {
+ ProjectionParameters projectionParameter = projectionParameters.get( 0 );
+ RandomAccessibleInterval<T> channelImg = Views.hyperSlice( input, 2, k );
+ Img<T> subVolume = ReferenceSurfaceProjection.getSubStack( channelImg, input.factory(),zMap, projectionParameter.getDelta(), projectionParameter.getOffset());
+
+ Img<T> p = ReferenceSurfaceProjection.run( subVolume, projectionParameter.getProjectionMethod() );
+ channelProjections.add(k, p );
+ }
+ Img<T> temp = ReferenceSurfaceProjection.regroupChannels( channelProjections );
+ String projectionName = String.format( "%s_proj_%d", inputName, (j+1) );
+ ImgPlus< T > finalProjection = ReferenceSurfaceProjection.setColorsAndName( temp, colorTables, projectionName );
+ finalProjections.add( finalProjection );
+ }
+ ImgSaver saver = new ImgSaver();
+ for ( int j = 0; j < referenceSurfaces.size(); j++ )
+ {
+ ImgPlus<T> projection = finalProjections.get(j);
+ String imgLocation = String.format( "%s\\%s%s",outputPath , projection.getName(), ".tif");
+ saver.saveImg(imgLocation, projection ) ;
+ }
+ LOGGER.debug("End of process");
+ fileAppender.stop();
+ }
+ }
+ catch ( TimeLapseException e )
+ {
+ throw new RuntimeException( e );
+ }
+ catch ( DataValidationException e )
+ {
+ throw new RuntimeException( e );
+ }
+ catch ( NoSurfaceFoundException e )
+ {
+ throw new RuntimeException( e );
+ }
+ catch ( NoClassificationException e )
+ {
+ throw new RuntimeException( e );
+ }
+ catch ( ImageTooLargeException e )
+ {
+ throw new RuntimeException( e );
+ }
+ catch ( NoA3DStackException e )
+ {
+ throw new RuntimeException( e );
+ }
+
+ }
+ /**
+ * Creates a new LogAppender to display the program state in the GUI.
+ */
+ public static void setLogStatus()
+ {
+ LoggerContext context = ( LoggerContext ) LoggerFactory.getILoggerFactory();
+ ch.qos.logback.classic.Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME);
+
+ // Encoder
+ PatternLayoutEncoder encoder = new PatternLayoutEncoder();
+ encoder.setContext( context );
+ encoder.setPattern( "%msg%n" );
+ encoder.start();
+
+ // Creates a new FileAppender
+ fileAppender = new LogFile();
+ fileAppender.setContext( context );
+ fileAppender.setFile( ".\\log.txt" );
+
+ fileAppender.setEncoder( encoder );
+ fileAppender.start();
+
+ // Attach the appender to the logger
+ rootLogger.addAppender( fileAppender );
+
+ }
+
+ public static void setLogFilePath(String path)
{
+ fileAppender.stop();
+ fileAppender.setFile( path );
+ fileAppender.start();
+ }
+ public static String uniqueID()
+ {
+ RandomStringGenerator generator = new RandomStringGenerator.Builder()
+ .withinRange('A', 'Z').get();
+ RandomStringGenerator generator2 = new RandomStringGenerator.Builder()
+ .withinRange('1', '9').get();
+ return String.format("_%s%s", generator.generate(2), generator2.generate(2));
+ }
+
+ public static class LogFile extends FileAppender< ILoggingEvent >
+ {
+ @Override
+ protected void append( ILoggingEvent iLoggingEvent )
+ {
+ String level = iLoggingEvent.getLevel().toString();
+ if ( level.equals( Level.INFO.toString() ) )
+ {
+ super.append(iLoggingEvent);
+ }
+
+ }
}
public static double getAdequacy()
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
index cd357d31e397415d839be8e4c4d00861a34f7ec6..92f61ad013791a992d3b9c45f77842929d3f1adb 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
@@ -38,8 +38,11 @@ import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
import javafx.application.Platform;
import javafx.fxml.FXML;
import javafx.fxml.Initializable;
+import javafx.scene.Scene;
import javafx.scene.control.*;
import javafx.stage.FileChooser;
+import javafx.stage.Modality;
+import javafx.stage.Stage;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import org.slf4j.Logger;
@@ -199,6 +202,23 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
}
}
+ @FXML
+ private void openFileDialog() {
+
+
+ BatchModeDialog dialog = new BatchModeDialog();
+
+ // Create a new Stage for the dialog
+ Stage dialogStage = new Stage();
+ dialogStage.setTitle("Batch Mode");
+ dialogStage.initModality( Modality.APPLICATION_MODAL); // Blocks interaction with main window
+ dialogStage.setScene(new Scene(dialog));
+
+ // Show the dialog window
+ dialogStage.showAndWait(); // Use showAndWait() to wait until the dialog is closed
+
+ }
+
private File chooseFile()
{
FileChooser fileChooser = chooseAFile( null, "Select a Zellige parameter file"
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
index 06a92646a139078a2e0116ee159053dd6735783b..109d1650aaeca87c2814157b6b03e6f3aa9a5175 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
@@ -23,7 +23,7 @@
<menus>
<Menu mnemonicParsing="false" text="File">
<items>
- <MenuItem mnemonicParsing="false" text="Batch Mode" />
+ <MenuItem mnemonicParsing="false" onAction="#openFileDialog" text="Batch Mode" />
</items>
</Menu>
<Menu mnemonicParsing="false" text="Edit">